Beveled cylinder cutout
[Blender 2.80]  I made an object similar to yours and discovered that applying a bevel to the edges "did" distort the walls of the cylinder when "all" surrounding edges were selected at once.  So I tried to apply the bevel to the edges in stages.  

First I beveled the 2 bottom edges (.05 amount), then just the sides and lastly the top edges and it worked... with just one division bevel.  I tried it again with a second window (same staged process).  This time I applied 2 bevel divisions and found that the corners were not well done.  But, with some manual refacing it worked.  It wasn't elegant, but it worked.  

This may or may not work for your needs.  And, I hope this is what you were referring to?